Fedora scientific packaging

[Sandro Mani]

Hello,

Some time ago I started working on packaging Salome, the platform for 
numerical simulation. As always, time is a limited resource, and things 
kinda stalled after hitting a few issues here and there, despite most of 
the work being done. Now, with Jiri Kastner joining the effort, we 
decided that it would be nice to attempt to make the effort of packaging 
scientific packages for Fedora in general more public, in particular 
considering the scientific-spin effort [1].
Many of the larger scientific packages tend to be very complex and their 
build systems occasionally somewhat fragile... So getting more 
interested people involved would likely increase the chances of the 
efforts succeeding.

That said, there is now a github repo which contains the 
work-in-progress stuff for packaging Salome (and some initial OpenFOAM 
work) here [2]. People interested in joining these efforts or sharing 
initial work on other scientific packages are very welcome to join the 
github project.

Best,
Sandro


[1] https://fedoraproject.org/wiki/Scientific_Spin
[2] https://github.com/fedora-scientific/

[M. Edward (Ed) Borasky]

The two I want most are RStudio (desktop and server) and R Commander.
RStudio does exist in RPM form but the packages are made via 'cmake' rather
than by Fedora's process, and the server's using the old school /etc/init.d
rather than systemd. R Commander's much easier - you just have to package
it's dependencies and deploy its desktop file.

When I get the time to work on a long-term project I may take a shot at
RStudio in COPR. OpenSUSE Build Service has source RPMs for RStudio but
they're many revisions old and seem to be unmaintained.

On Fri, Nov 21, 2014 at 11:32 AM, Sandro Mani <manisandro(a)gmail.com&gt; wrote:

>  Hello,
>
>  Some time ago I started working on packaging Salome, the platform for
>  numerical simulation. As always, time is a limited resource, and things
>  kinda stalled after hitting a few issues here and there, despite most of
>  the work being done. Now, with Jiri Kastner joining the effort, we decided
>  that it would be nice to attempt to make the effort of packaging scientific
>  packages for Fedora in general more public, in particular considering the
>  scientific-spin effort [1].
>  Many of the larger scientific packages tend to be very complex and their
>  build systems occasionally somewhat fragile... So getting more interested
>  people involved would likely increase the chances of the efforts succeeding.
>
>  That said, there is now a github repo which contains the work-in-progress
>  stuff for packaging Salome (and some initial OpenFOAM work) here [2].
>  People interested in joining these efforts or sharing initial work on other
>  scientific packages are very welcome to join the github project.
>
>  Best,
>  Sandro
>
>
>  [1] https://fedoraproject.org/wiki/Scientific_Spin
>  [2] https://github.com/fedora-scientific/
>
>  --
>  devel mailing list
>  devel(a)lists.fedoraproject.org
>  https://admin.fedoraproject.org/mailman/listinfo/devel
>  Fedora Code of Conduct: http://fedoraproject.org/code-of-conduct 



-- 
Twitter: http://twitter.com/znmeb; Computational Journalism on a Stick
http://j.mp/CompJournoStickOverview

Remember, if you're traveling to Bactria, Hump Day is Tuesday and Thursday.

[Pete Travis]

On Nov 21, 2014 12:48 PM, "M. Edward (Ed) Borasky" <znmeb(a)znmeb.net&gt;
wrote:
>  The two I want most are RStudio (desktop and server) and R Commander. 
RStudio does
exist in RPM form but the packages are made via 'cmake' rather
than by Fedora's process, and the server's using the old school /etc/init.d
rather than systemd. R Commander's much easier - you just have to package
it's dependencies and deploy its desktop file.
>  When I get the time to work on a long-term project I may take a shot at 
RStudio in
COPR. OpenSUSE Build Service has source RPMs for RStudio but
they're many revisions old and seem to be unmaintained.
>  
I don't have a personal interest in RStudio, but I do support users that
rave about it.  While not entirely enthusiastic about taking on packages
when I don't have much experience using the software, it wouldn't be so bad
to get things rolling with a comaintainer that does have that experience.
Bonus, its one more thing to check off my "We can't use Linux because...."
list.

What do you say, Ed?  If I get the package review done, will you help with
bugs and maintenance?

--Pete

[Suchakra]

Hi,

>  What do you say, Ed?  If I get the package review done, will you help
> with
>  bugs and maintenance?
>
>  --Pete 
I am using RStudio actively on Fedora using the rpm they provide.
Though it works just about satisfactorily for me standalone,  it would
really be nice to have it in our repos. I can help in testing/bugs and
occasional maintenance.

--
Suchakra

[M. Edward (Ed) Borasky]

I think the Fedora policy requires more of a commitment from maintainers
than I can offer. In any event, I know RStudio Server can be built from
source on Fedora and that it works but it needs a lot of detailed attention
to turn it into something that will make it into a release. It has a few
dependencies - gwt, for one - that aren't in Fedora so their source needs
to be packaged in the source RPM.

There's also the question of upstream - they have a build process that
makes usable binaries for openSUSE and Fedora but only support the server
on Debian, Ubuntu, RHEL and CentOS. I did get them to fix some issues when
their run-time dependencies messed up a Fedora R upgrade, but I don't know
if they'd actively participate in a distro packaging effort. They'd need to
be asked.

All that said, this is a good time to start such a project, since Fedora 21
is about two weeks away from release. I have a COPR project opened but
haven't put anything in it yet -
https://copr.fedoraproject.org/coprs/znmeb/rstudio/

On Fri, Nov 21, 2014 at 8:38 PM, Suchakra <suchakra(a)fedoraproject.org&gt;
wrote:

>  Hi,
>
>  > What do you say, Ed?  If I get the package review done, will you help
>  with
>  > bugs and maintenance?
>  >
>  > --Pete
>
>  I am using RStudio actively on Fedora using the rpm they provide.
>  Though it works just about satisfactorily for me standalone,  it would
>  really be nice to have it in our repos. I can help in testing/bugs and
>  occasional maintenance.
>
>  --
>  Suchakra
>  --
>  devel mailing list
>  devel(a)lists.fedoraproject.org
>  https://admin.fedoraproject.org/mailman/listinfo/devel
>  Fedora Code of Conduct: http://fedoraproject.org/code-of-conduct
>  


-- 
Twitter: http://twitter.com/znmeb; Computational Journalism on a Stick
http://j.mp/CompJournoStickOverview

Remember, if you're traveling to Bactria, Hump Day is Tuesday and Thursday.

[Pete Travis]

On 11/21/2014 11:22 PM, M. Edward (Ed) Borasky wrote:
>  I think the Fedora policy requires more of a commitment from
>  maintainers than I can offer. In any event, I know RStudio Server can
>  be built from source on Fedora and that it works but it needs a lot of
>  detailed attention to turn it into something that will make it into a
>  release. It has a few dependencies - gwt, for one - that aren't in
>  Fedora so their source needs to be packaged in the source RPM.
>
>  There's also the question of upstream - they have a build process that
>  makes usable binaries for openSUSE and Fedora but only support the
>  server on Debian, Ubuntu, RHEL and CentOS. I did get them to fix some
>  issues when their run-time dependencies messed up a Fedora R upgrade,
>  but I don't know if they'd actively participate in a distro packaging
>  effort. They'd need to be asked.
>
>  All that said, this is a good time to start such a project, since
>  Fedora 21 is about two weeks away from release. I have a COPR project
>  opened but haven't put anything in it yet -
>  https://copr.fedoraproject.org/coprs/znmeb/rstudio/
>
>  On Fri, Nov 21, 2014 at 8:38 PM, Suchakra <suchakra(a)fedoraproject.org
>  <mailto:[e-mail]>> wrote:
>
>      Hi,
>
>      > What do you say, Ed?  If I get the package review done, will you
>      help with
>      > bugs and maintenance?
>      >
>      > --Pete
>
>      I am using RStudio actively on Fedora using the rpm they provide.
>      Though it works just about satisfactorily for me standalone,  it would
>      really be nice to have it in our repos. I can help in testing/bugs and
>      occasional maintenance.
>
>      --
>      Suchakra
>      --
>      devel mailing list
>      devel(a)lists.fedoraproject.org <mailto:[e-mail]>
>      https://admin.fedoraproject.org/mailman/listinfo/devel
>      Fedora Code of Conduct: http://fedoraproject.org/code-of-conduct
>
>
>
>
>  -- 
>  Twitter: http://twitter.com/znmeb; Computational Journalism on a Stick
>  http://j.mp/CompJournoStickOverview
>
>  Remember, if you're traveling to Bactria, Hump Day is Tuesday and
>  Thursday.
>
>  
I just glanced at their github repo.. wow. 
https://github.com/rstudio/rstudio/releases - it looks like they are
tagging a 'release' every time they touch the code.  There's also a lot
of bundling; probably not an insurmountable amount, but it won't be an
easy one to package.

As for upstream suppport... well, the bundling is indicative of how
they'd probably feel about keeping up with our dependency churn.  It
isn't uncommon for upstreams to not actively participate in the
packaging process, but if they're taking the stance where 'we only
support the latest release (ha!) with these specific versions of deps'
it would be a nightmare. Detailed attention is right :)

Anyway, I'll keep an eye on this thread and if there's enough interest,
I'll happily participate in the packaging.  Still definitely more than I
want to take on alone - but it does look like an interesting challenge.

-- 
-- Pete

[Scitech] Fedora scientific packaging

[Dave Love]

Sandro Mani <manisandro(a)gmail.com&gt; writes:

>  That said, there is now a github repo which contains the
>  work-in-progress stuff for packaging Salome (and some initial OpenFOAM
>  work) here [2]. People interested in joining these efforts or sharing
>  initial work on other scientific packages are very welcome to join the
>  github project. 
For what it's worth, there's an OpenFOAM package installing into /opt
under <http://copr.fedoraproject.org/coprs/loveshack/livhpc/> which is
OK for people who need it on HPC systems.  I don't know whether it would
satisfy packaging requirements simply to move it under MPI_HOME
wholesale.  Possibly relevant to Salome, I have an unpublished package
of code_saturne, but I had trouble getting it working with multiple
MPIs.

[Zbigniew Jędrzejewski-Szmek]

I have working packages [1] for genesis and moose
(both neuron simulators). I didn't submit them because
genesis is old and buggy, and moose a bit unstable, but
with the release of v. 3 I'll submit it as a Fedora package.
I'm now working on pysb and bionetgen as a dependency. Apart
from some bundling which is relatively easy to undo, everything
seems nice and simple.

[1] http://copr-fe.cloud.fedoraproject.org/coprs/zbyszek/neurord

Zbyszek

[Zbigniew Jędrzejewski-Szmek]

On Sat, Nov 22, 2014 at 10:12:46PM +0100, Zbigniew Jędrzejewski-Szmek wrote:
>  I have working packages [1] for genesis and moose
>  (both neuron simulators). I didn't submit them because
>  genesis is old and buggy, and moose a bit unstable, but
>  with the release of v. 3 I'll submit it as a Fedora package.
>  I'm now working on pysb and bionetgen as a dependency. Apart
>  from some bundling which is relatively easy to undo, everything
>  seems nice and simple. 
python-pygraphviz [1], bionetgen [2], and python-pysb [3]
are now ready.
Reviewers very much welcome, altruistic or barter (swap) based.

[1] https://bugzilla.redhat.com/show_bug.cgi?id=1167460
[2] https://bugzilla.redhat.com/show_bug.cgi?id=1167467
[3] https://bugzilla.redhat.com/show_bug.cgi?id=1167478

Zbyszek

[Mukundan Ragavan]

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

On 11/24/2014 03:49 PM, Zbigniew Jędrzejewski-Szmek wrote:
>  On Sat, Nov 22, 2014 at 10:12:46PM +0100, Zbigniew
>  Jędrzejewski-Szmek wrote:
> > I have working packages [1] for genesis and moose (both neuron
> > simulators). I didn't submit them because genesis is old and
> > buggy, and moose a bit unstable, but with the release of v. 3
> > I'll submit it as a Fedora package. I'm now working on pysb and
> > bionetgen as a dependency. Apart from some bundling which is
> > relatively easy to undo, everything seems nice and simple.
>  python-pygraphviz [1], bionetgen [2], and python-pysb [3] are now
>  ready. Reviewers very much welcome, altruistic or barter (swap)
>  based.
>  
>  [1] https://bugzilla.redhat.com/show_bug.cgi?id=1167460 [2]
>  https://bugzilla.redhat.com/show_bug.cgi?id=1167467 [3]
>  https://bugzilla.redhat.com/show_bug.cgi?id=1167478
>  
>  Zbyszek
>   
Well, I can review all these three packages. We have break coming up
(from Thursday) and I can review it that day.

I am assigning the bugs to myself. If someone wants to go review the
packages before I get to it, please go ahead.

Mukundan.

- -- 
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[Zbigniew Jędrzejewski-Szmek]

On Mon, Nov 24, 2014 at 07:21:03PM -0600, Mukundan Ragavan wrote:
>  -----BEGIN PGP SIGNED MESSAGE-----
>  Hash: SHA512
>  
>  On 11/24/2014 03:49 PM, Zbigniew Jędrzejewski-Szmek wrote:
>  > On Sat, Nov 22, 2014 at 10:12:46PM +0100, Zbigniew
>  > Jędrzejewski-Szmek wrote:
>  >> I have working packages [1] for genesis and moose (both neuron
>  >> simulators). I didn't submit them because genesis is old and
>  >> buggy, and moose a bit unstable, but with the release of v. 3
>  >> I'll submit it as a Fedora package. I'm now working on pysb and
>  >> bionetgen as a dependency. Apart from some bundling which is
>  >> relatively easy to undo, everything seems nice and simple.
>  > python-pygraphviz [1], bionetgen [2], and python-pysb [3] are now
>  > ready. Reviewers very much welcome, altruistic or barter (swap)
>  > based.
>  > 
>  > [1] https://bugzilla.redhat.com/show_bug.cgi?id=1167460 [2]
>  > https://bugzilla.redhat.com/show_bug.cgi?id=1167467 [3]
>  > https://bugzilla.redhat.com/show_bug.cgi?id=1167478
>  > 
>  > Zbyszek
>  > 
>  
>  Well, I can review all these three packages. We have break coming up
>  (from Thursday) and I can review it that day. 
Great, thanks.

Zbyszek

[Amit Saha]

----- Original Message -----
>  From: "Sandro Mani" <manisandro(a)gmail.com&gt;
>  To: "Development discussions related to Fedora"
> <devel(a)lists.fedoraproject.org&gt;, scitech(a)lists.fedoraproject.org
>  Sent: Saturday, November 22, 2014 5:32:43 AM
>  Subject: Fedora scientific packaging
>  
>  Hello,
>  
>  Some time ago I started working on packaging Salome, the platform for
>  numerical simulation. As always, time is a limited resource, and things
>  kinda stalled after hitting a few issues here and there, despite most of
>  the work being done. Now, with Jiri Kastner joining the effort, we
>  decided that it would be nice to attempt to make the effort of packaging
>  scientific packages for Fedora in general more public, in particular
>  considering the scientific-spin effort [1].
>  Many of the larger scientific packages tend to be very complex and their
>  build systems occasionally somewhat fragile... So getting more
>  interested people involved would likely increase the chances of the
>  efforts succeeding.
>  
>  That said, there is now a github repo which contains the
>  work-in-progress stuff for packaging Salome (and some initial OpenFOAM
>  work) here [2]. People interested in joining these efforts or sharing
>  initial work on other scientific packages are very welcome to join the
>  github project. 

This is great. I created the Fedora Scientific organization on GitHub some time back [1].
Do you think you would want to get your repo moved here? I can of course make you an
admin,
member, etc.

[1] https://github.com/FedoraScientific

Thanks,
Amit.